BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094152.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 47,854 number of mapped reads = 5,293 (11.06%) number of supplementary alignments = 65 (0.14%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,492 number of mapped paired reads (second in pair) = 2,801 number of mapped paired reads (both in pair) = 4,802 number of mapped paired reads (singletons) = 491 number of mapped bases = 705,251 bp number of sequenced bases = 702,403 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,756 duplication rate = 28.07% >>>>>>> Insert size mean insert size = 87,474.0944 std insert size = 2,547,002.9963 median insert size = 233 >>>>>>> Mapping quality mean mapping quality = 6.9759 >>>>>>> ACTG content number of A's = 180,826 bp (25.74%) number of C's = 134,295 bp (19.12%) number of T's = 196,789 bp (28.02%) number of G's = 190,468 bp (27.12%) number of N's = 25 bp (0%) GC percentage = 46.24% >>>>>>> Mismatches and indels general error rate = 0.0239 number of mismatches = 16,152 number of insertions = 129 mapped reads with insertion percentage = 2% number of deletions = 856 mapped reads with deletion percentage = 14.94% homopolymer indels = 31.88% >>>>>>> Coverage mean coverageData = 0.0002X std coverageData = 0.4689X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1472 5.905702437547788E-6 0.0030913771904686484 chr2 243199373 39354 1.6181785139717444E-4 0.15644842677398457 chr3 198022430 508 2.565365953745745E-6 0.0016016739283147704 chr4 191154276 585 3.0603552912413007E-6 0.0020444707165031303 chr5 180915260 915 5.057616477460221E-6 0.0039263254627947605 chr6 171115067 8377 4.895536171575119E-5 0.04797914421820656 chr7 159138663 774 4.863682937941989E-6 0.0027299444048608703 chr8 146364022 841 5.745947593596464E-6 0.004026533026774991 chr9 141213431 30138 2.1342162559593924E-4 0.19947965454213473 chr10 135534747 1171 8.639850856843374E-6 0.004873427180340289 chr11 135006516 13347 9.886189493253792E-5 0.08635997377308126 chr12 133851895 586 4.377973132169701E-6 0.002398459431644946 chr13 115169878 307 2.665627552370942E-6 0.0017407754406433954 chr14 107349540 418 3.893821994952191E-6 0.003295709153440203 chr15 102531392 1260 1.2288919280448274E-5 0.00632203299968991 chr16 90354753 2888 3.196290072310861E-5 0.019257424148309835 chr17 81195210 19299 2.376864349510273E-4 0.17120505637755098 chr18 78077248 185 2.369448267438934E-6 0.0017929749949032398 chr19 59128983 139 2.3507930112716466E-6 0.0015332277994622538 chr20 63025520 114 1.8087911055712036E-6 0.0013449118312536105 chr21 48129895 0 0.0 0.0 chr22 51304566 235 4.580488995852728E-6 0.0021402027976276656 chrMT 16571 390970 23.59362742139883 178.15800177906578 chrX 155270560 190583 0.0012274252118366804 0.9150514739347991 chrY 59373566 785 1.3221371948587357E-5 0.005598549386886907